Proxl is a database and web application for viewing, analyzing, and sharing bottom-up
proteomics data resulting from chemical crosslinking and mass spectrometry
analysis. It includes tools for viewing, downloading, and visualizing data; including tools
for comparing data between different searches and pipelines.

If downloaded and installed privately, the site administrator may choose to allow public registration (see above)
or restrict access to only those who are invited to projects.

If restricted to invites-only, the only way to gain access to a proxl installation is to be invited to a project by an
existing user. Only users associated with a project may invite users to the project.
(To learn how to invite a user to a project, see Researchers.)
Invitations will appear in your email with a link to register as a user of proxl.
Important: Be sure to check your SPAM folder for proxl invitations if they do not appear.

Unless you are already logged into proxl, following the link in the invitation email
brings you to the following screen. (If you are already logged in, you will be taken to a list of
you projects, which now includes the one to which you were invited.)

Choosing “Sign In” will sign you into proxl, and the new project will be listed in your
project list. Choosing “Create Account” will present you with the following registration form:

Filling out this form will create a new account, log you in, and display the project
to which you were invited in your project list.

If you are unable to remember your password, click the “Reset Password” button at the
bottom-right of the sign-in form. Entering either your username or email address on file
for your account will send a link to your email address that may be used to reset
your password. For security reasons, this link is only valid for 24 hours.

Projects in proxl are the core means of organizing data and controlling access to those
data. While projects serve to logically organize data by theme or aim,
they also serve to organize the data by who you would like to have access
to those data. All data are associated with projects and, by default, only the researchers
associated with a project may view data associated with that project. (These permissions
can be changed, see Public Access.)

Once logged in, you will be presented with a list of projects that you may currently access.
For example:

In this example, the user has access to three projects. Clicking on the titles of any of
these projects will navigate to that project and its data. From any page, the user may
also mouse over (or tap on mobile devices) the “Projects” text at the top page to
see a drop-down list of project titles. Clicking on any of these will navigate to that
project’s page and data:

Click on “(+) New Project” above the project list to add a new project by
supplying a title and (optionally) an abstract for your project. Once the project
is added, it will appear in the project list with the supplied title. Click on the
project title to navigate to that project’s overview page to manage access and
add researchers to the project. (See “Researchers.)

Click the red (X) icon to the left of the project title on the project list to delete
that project. Only project owners may delete projects. Once a project is deleted,
the project and all associated data will be removed.